2 - Specify which NMDS dimensions to plot when there are more than two available.

Using the nmds function in the ECODIST package, when evaluating more than two dimensions, all possible pair-wise combinations of dimensions are shown by default when using the plot function. In this example, only two specific dimensions are chosen for plotting.

In the plot function, the x-y coordinates from the nmds.min object can be chosen and plotted.

Sample R commands: To plot NMDS2 and NMDS3 only.

nmds.object<-nmds(distancematrix)

nmds.min.object<-nmds.min(nmds.object)

plot(nmds.min.object$X2, nmds.min.object$X3, xlab="NMDS2",ylab="NMDS3", bty="n")